protocols::stepwise::modeler::options::StepWiseProteinModelerOptions Class Reference

#include <StepWiseProteinModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseProteinModelerOptions:

Public Member Functions
	StepWiseProteinModelerOptions ()
StepWiseProteinModelerOptionsOP	clone () const
	clone the options More...
virtual void	show (std::ostream &) const
	Describe this instance to a given output stream. More...
virtual void	parse_my_tag (utility::tag::TagCOP)
	Initialize from the recursive "tag" structure. More...
virtual std::string	type () const
	The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery. More...
void	initialize_from_command_line ()
void	set_global_optimize (bool const &setting)
bool	global_optimize () const
void	set_sample_beta (bool const &setting)
bool	sample_beta () const
void	set_move_jumps_between_chains (bool const &setting)
bool	move_jumps_between_chains () const
void	set_disable_sampling_of_loop_takeoff (bool const &setting)
bool	disable_sampling_of_loop_takeoff () const
void	set_cart_min (bool const &setting)
bool	cart_min () const
void	set_n_sample (core::Size const &setting)
core::Size	n_sample () const
void	set_filter_native_big_bins (bool const &setting)
bool	filter_native_big_bins () const
void	set_allow_virtual_side_chains (bool const &setting)
bool	allow_virtual_side_chains () const
void	set_prepack (bool const &setting)
bool	prepack () const
void	set_pack_protein_side_chains (bool const &setting)
bool	pack_protein_side_chains () const
void	set_centroid_output (bool const &setting)
bool	centroid_output () const
void	set_centroid_screen (bool const &setting)
bool	centroid_screen () const
void	set_centroid_score_diff_cut (core::Real const &setting)
core::Real	centroid_score_diff_cut () const
void	set_centroid_weights (std::string const &setting)
std::string	centroid_weights () const
void	set_nstruct_centroid (core::Size const &setting)
core::Size	nstruct_centroid () const
void	set_ghost_loops (bool const &setting)
bool	ghost_loops () const
void	set_ccd_close (bool const &setting)
bool	ccd_close () const
void	set_cluster_by_all_atom_rmsd (bool const &setting)
bool	cluster_by_all_atom_rmsd () const
void	set_pack_weights (std::string const &setting)
std::string	pack_weights () const
bool const &	expand_loop_takeoff () const
void	set_expand_loop_takeoff (bool const &setting)
bool const &	skip_coord_constraints () const
void	set_skip_coord_constraints (bool const &setting)
void	set_frag_files (utility::vector1< std::string > const &setting)
utility::vector1< std::string >	frag_files () const
void	set_bridge_res (utility::vector1< core::Size > const &setting)
utility::vector1< core::Size >	bridge_res () const

Protected Member Functions
void	initialize_variables ()

Private Attributes
bool	global_optimize_
bool	sample_beta_
bool	move_jumps_between_chains_
bool	disable_sampling_of_loop_takeoff_
bool	cart_min_
core::Size	n_sample_
bool	filter_native_big_bins_
bool	allow_virtual_side_chains_
bool	prepack_
bool	pack_protein_side_chains_
bool	centroid_output_
bool	centroid_screen_
core::Real	centroid_score_diff_cut_
std::string	centroid_weights_
core::Size	nstruct_centroid_
bool	ghost_loops_
bool	ccd_close_
bool	cluster_by_all_atom_rmsd_
std::string	pack_weights_
bool	expand_loop_takeoff_
bool	skip_coord_constraints_
utility::vector1< std::string >	frag_files_
utility::vector1< core::Size >	bridge_res_

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::StepWiseProteinModelerOptions

(

)

Member Function Documentation

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains ( ) const

inline

References allow_virtual_side_chains_.

utility::vector1< core::Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res ( ) const

inline

References bridge_res_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min ( ) const

inline

References cart_min_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close ( ) const

inline

References ccd_close_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output ( ) const

inline

References centroid_output_.

core::Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut ( ) const

inline

References centroid_score_diff_cut_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen ( ) const

inline

References centroid_screen_.

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights ( ) const

inline

References centroid_weights_.

StepWiseProteinModelerOptionsOP protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::clone

(

)

const

clone the options

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cluster_by_all_atom_rmsd ( ) const

inline

References cluster_by_all_atom_rmsd_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::disable_sampling_of_loop_takeoff ( ) const

inline

References disable_sampling_of_loop_takeoff_.

bool const& protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::expand_loop_takeoff ( ) const

inline

References expand_loop_takeoff_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::filter_native_big_bins ( ) const

inline

References filter_native_big_bins_.

utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::frag_files ( ) const

inline

References frag_files_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops ( ) const

inline

References ghost_loops_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize ( ) const

inline

References global_optimize_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_from_command_line

(

)

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_variables ( )

protected

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains ( ) const

inline

References move_jumps_between_chains_.

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample ( ) const

inline

References n_sample_.

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid ( ) const

inline

References nstruct_centroid_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_protein_side_chains ( ) const

inline

References pack_protein_side_chains_.

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights ( ) const

inline

References pack_weights_.

virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::parse_my_tag ( utility::tag::TagCOP  )

inlinevirtual

Initialize from the recursive "tag" structure.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack ( ) const

inline

References prepack_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta ( ) const

inline

References sample_beta_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_allow_virtual_side_chains ( bool const &  setting )

inline

References allow_virtual_side_chains_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_bridge_res ( utility::vector1< core::Size > const &  setting )

inline

References bridge_res_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cart_min ( bool const &  setting )

inline

References cart_min_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ccd_close ( bool const &  setting )

inline

References ccd_close_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_output ( bool const &  setting )

inline

References centroid_output_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_score_diff_cut ( core::Real const &  setting )

inline

References centroid_score_diff_cut_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_screen ( bool const &  setting )

inline

References centroid_screen_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_weights ( std::string const &  setting )

inline

References centroid_weights_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cluster_by_all_atom_rmsd ( bool const &  setting )

inline

References cluster_by_all_atom_rmsd_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_disable_sampling_of_loop_takeoff ( bool const &  setting )

inline

References disable_sampling_of_loop_takeoff_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_expand_loop_takeoff ( bool const &  setting )

inline

References expand_loop_takeoff_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_filter_native_big_bins ( bool const &  setting )

inline

References filter_native_big_bins_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_frag_files ( utility::vector1< std::string > const &  setting )

inline

References frag_files_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ghost_loops ( bool const &  setting )

inline

References ghost_loops_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_global_optimize ( bool const &  setting )

inline

References global_optimize_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_move_jumps_between_chains ( bool const &  setting )

inline

References move_jumps_between_chains_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_n_sample ( core::Size const &  setting )

inline

References n_sample_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_nstruct_centroid ( core::Size const &  setting )

inline

References nstruct_centroid_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_protein_side_chains ( bool const &  setting )

inline

References pack_protein_side_chains_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_weights ( std::string const &  setting )

inline

References pack_weights_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_prepack ( bool const &  setting )

inline

References prepack_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_sample_beta ( bool const &  setting )

inline

References sample_beta_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_skip_coord_constraints ( bool const &  setting )

inline

References skip_coord_constraints_.

virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::show ( std::ostream &  ) const

inlinevirtual

Describe this instance to a given output stream.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool const& protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints ( ) const

inline

References skip_coord_constraints_.

virtual std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::type ( ) const

inlinevirtual

The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains_

private

Referenced by allow_virtual_side_chains(), and set_allow_virtual_side_chains().

utility::vector1< core::Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res_

private

Referenced by bridge_res(), and set_bridge_res().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min_

private

Referenced by cart_min(), and set_cart_min().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close_

private

Referenced by ccd_close(), and set_ccd_close().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output_

private

Referenced by centroid_output(), and set_centroid_output().

core::Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut_

private

Referenced by centroid_score_diff_cut(), and set_centroid_score_diff_cut().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen_

private

Referenced by centroid_screen(), and set_centroid_screen().

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights_

private

Referenced by centroid_weights(), and set_centroid_weights().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cluster_by_all_atom_rmsd_

private

Referenced by cluster_by_all_atom_rmsd(), and set_cluster_by_all_atom_rmsd().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::disable_sampling_of_loop_takeoff_

private

Referenced by disable_sampling_of_loop_takeoff(), and set_disable_sampling_of_loop_takeoff().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::expand_loop_takeoff_

private

Referenced by expand_loop_takeoff(), and set_expand_loop_takeoff().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::filter_native_big_bins_

private

Referenced by filter_native_big_bins(), and set_filter_native_big_bins().

utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::frag_files_

private

Referenced by frag_files(), and set_frag_files().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops_

private

Referenced by ghost_loops(), and set_ghost_loops().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize_

private

Referenced by global_optimize(), and set_global_optimize().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains_

private

Referenced by move_jumps_between_chains(), and set_move_jumps_between_chains().

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample_

private

Referenced by n_sample(), and set_n_sample().

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid_

private

Referenced by nstruct_centroid(), and set_nstruct_centroid().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_protein_side_chains_

private

Referenced by pack_protein_side_chains(), and set_pack_protein_side_chains().

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights_

private

Referenced by pack_weights(), and set_pack_weights().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack_

private

Referenced by prepack(), and set_prepack().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta_

private

Referenced by sample_beta(), and set_sample_beta().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints_

private

Referenced by set_skip_coord_constraints(), and skip_coord_constraints().

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The documentation for this class was generated from the following files:

• src/protocols/stepwise/modeler/options/StepWiseProteinModelerOptions.hh
• src/protocols/stepwise/modeler/options/StepWiseProteinModelerOptions.cc